WNT family genes encode WNT family glycoproteins, while Frizzled (FZD) family genes encode seven-transmembrane-type receptors with extracellular WNT-binding domain and cytoplasmic Dishevelled-binding domain. WNT signaling pathway is implicated in carcinogenesis and embryogenesis. WNT1-WNT10B, WNT6-WNT10A, WNT3-WNT9B (WNT14B), WNT3A-WNT9A (WNT14) gene clusters exist within the human genome. Here, we identified and characterized rat Wnt1 and Wnt10b genes by using bioinformatics. Rat Wnt1 gene, consisting of four exons, encoded a 370-aa protein with signal peptide, 22 conserved Cys residues and four Asn-linked glycosylation sites. Rat Wnt10b gene, consisting of five exons, encoded a 389-aa protein with signal peptide, 24 conserved Cys residues and two Asn-linked glycosylation sites. Wnt1 and Wnt10b genes at rat chromosome 7q36 were clustered in head-to-head manner with an interval of about 10 kb within AC096835.4 or AC118760.4 genome sequences. Promoter region, exon 1 and 5'-part of intron 1 were conserved between rat and human Wnt1 orthologs. Intergenic conserved region (IGCR) was identified within the Wnt1-Wnt10b gene cluster. GC content of rat Wnt1-Wnt10b IGCR (nucleotide position 14962-15875 of AC096835.4 genome sequence) was 59.4%. Rat Wnt1-Wnt10b IGCR showed 92.5 and 74.4% nucleotide identity with mouse Wnt1-Wnt10b IGCR and human WNT1-WNT10B IGCR, respectively. Wnt1-Wnt10b IGCR was predicted as regulatory element rather than gene because cDNA or EST derived from Wnt1-Wnt10b IGCR was not identified. This is the first report on rat Wnt1 and Wnt10b genes as well as on Wnt1-Wnt10b IGCR.